Abstract 2019: NCI’s clinical proteomic tumor analysis consortium analysis tools and resources
Authors: Mehdi Mesri, Eunkyung An, Xu Zhang, Jasmin Bavarva, Ana I. Robles, Tara Hiltke, Henry Rodriguez
Journal: Cancer Research (2023)

Abstract The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI’s CPTAC) is an integrative proteogenomic program composed of a Tumor Characterization Program and a Translational Research Program (PTRC) (https://proteomics.cancer.gov). The CPTAC aims to leverage the investments made in cancer research by understanding the molecular changes by proteogenomically characterizing cancers and accelerating the basic discovery toward clinical impact. This goal is achieved through the application of large-scale proteome and genome analyses, followed by proteogenomic integration of genome, transcriptome, and proteome data sets. Together, it enables the correlation analysis of mRNA and protein, mutations, post-translational modifications, and signaling pathways. All data and analytical tools are made broadly available to the research community through public databases to maximize utility and public benefit. CPTAC teams have characterized a multitude of treatment-naïve tumor types, including colorectal, ovarian, breast, clear cell renal cell carcinoma, uterine corpus endometrial carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, brain (including adult, pediatric, and adolescent and young adult), head and neck squamous cell carcinoma, and pancreatic ductal adenocarcinoma (https://proteomics.cancer.gov/resources/milestones-and-publications). Ongoing projects include acute myeloid leukemia (AML), cutaneous melanoma, sarcoma, oligodendroglioma, and stomach cancers. In the PTRC Program, CPTAC is partnering with NCI-sponsored clinical trials to support clinically relevant research projects that would elucidate biological mechanisms of therapeutic response, resistance, and/or toxicity. The PTRC Program currently explores breast, ovarian, AML, multiple myeloma, melanoma, and lung cancers. All mass spectrometry-based proteomic, genomic, and imaging data (histopathology and radiology) are made publicly available at the CPTAC Proteomic Data Commons (https://pdc.cancer.gov), Genomic Data Commons (https://gdc.cancer.gov), and the Cancer Imaging Archive (https://cancerimagingarchive.net) respectively. CPTAC is also supporting development of new proteogenomic data analysis tools (https://proteomics.cancer.gov/resources/computational-tools). In addition, the CPTAC Assay Portal (http://assays.cancer.gov) is a public resource populated with mass spectrometry-based targeted proteomic assays developed by the consortium for quantitatively measuring proteins of interest, including those discovered through comprehensive tumor characterization. Lastly, well-characterized monoclonal antibodies targeting cancer-specific proteins and peptides are also made available at CPTAC’s Antibody Portal (http://antibodies.cancer.gov). Citation Format: Mehdi Mesri, Eunkyung An, Xu Zhang, Jasmin Bavarva, Ana I. Robles, Tara Hiltke, Henry Rodriguez. NCI’s clinical proteomic tumor analysis consortium analysis tools and resources [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2019.